Re: [gmx-users] Can't observe ion separation under the influence of electric field
Hi Live King, I think the temperature coupling strongly effect on your observation since the velocity of atoms (ions) will be rescale after every tau-t value. It means the movement direction of ion under EEF will be mostly canceled for every tau-t (ps). If you set tau-t to be larger than default value (.i.e 10, 100 or 1000) you can see the effect of EEF on your system. Viet Man, University of Pittsburgh School of Pharmacy > > Dear David and Harutyun, > > Thanks for your reply. Density plots were the first check I did. They show > a very minor difference. I imagined that the electric field is not > sufficient, however, presence of high electric field ( > 1 V or 1000mV)* > disrupts the membrane and my simulation crashes*. Is there any solution to > this problem? I will have a look at compel. > > On Thu, Feb 13, 2020 at 6:21 PM Harutyun Sahakyan > wrote: > >> You can use compel and build a double bilayer system to separate ions. >> However, if you separate positive and negative ions, you will have very >> high membrane potential, event two ions difference can raise potential >> about 200 mV. In your case, I suppose 500 mV is not enough to separate >> all >> ions in a PBC box. >> >> https://www.mpibpc.mpg.de/grubmueller/compel >> >> >> >> Harutyun Sahakyan >> Senior Assistant at Laboratory of >> Computational Modeling of Biological Processes, >> Institute of Molecular Biology, NAS, Armenia, Yerevan >> Tel: +374 93 323990 >> h_sahak...@mb.sci.am >> sahakya...@gmail.com >> >> February 13, 2020 2:07 AM, "Live King" wrote: >> >> > Dear all, >> > >> > I am running a simple test case with a lipid bilayer (DMPC), water, >> and >> > ions (150mM KCL) under the influence of a constant electric field ( >> 300mV, >> > 500mV, and 700mV). *I expected positive and negative ions to separate >> in >> > the presence of an external electric field*. However, I am not >> observing >> > such behavior despite running the all-atom simulation for 400ns in any >> > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui >> > production with electric field option. >> > >> > for example 500mV electric field in Z-direction : >> > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = >> > 500 mV * >> > >> > Are there any settings to run the electric field simulation that I >> miss? >> > Any help will be greatly appreciated. >> > >> > Thank you, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can't observe ion separation under the influence of electric field
Dear David and Harutyun, Thanks for your reply. Density plots were the first check I did. They show a very minor difference. I imagined that the electric field is not sufficient, however, presence of high electric field ( > 1 V or 1000mV)* disrupts the membrane and my simulation crashes*. Is there any solution to this problem? I will have a look at compel. On Thu, Feb 13, 2020 at 6:21 PM Harutyun Sahakyan wrote: > You can use compel and build a double bilayer system to separate ions. > However, if you separate positive and negative ions, you will have very > high membrane potential, event two ions difference can raise potential > about 200 mV. In your case, I suppose 500 mV is not enough to separate all > ions in a PBC box. > > https://www.mpibpc.mpg.de/grubmueller/compel > > > > Harutyun Sahakyan > Senior Assistant at Laboratory of > Computational Modeling of Biological Processes, > Institute of Molecular Biology, NAS, Armenia, Yerevan > Tel: +374 93 323990 > h_sahak...@mb.sci.am > sahakya...@gmail.com > > February 13, 2020 2:07 AM, "Live King" wrote: > > > Dear all, > > > > I am running a simple test case with a lipid bilayer (DMPC), water, and > > ions (150mM KCL) under the influence of a constant electric field ( > 300mV, > > 500mV, and 700mV). *I expected positive and negative ions to separate in > > the presence of an external electric field*. However, I am not observing > > such behavior despite running the all-atom simulation for 400ns in any > > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui > > production with electric field option. > > > > for example 500mV electric field in Z-direction : > > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = > > 500 mV * > > > > Are there any settings to run the electric field simulation that I miss? > > Any help will be greatly appreciated. > > > > Thank you, > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to > > gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can't observe ion separation under the influence of electric field
You can use compel and build a double bilayer system to separate ions. However, if you separate positive and negative ions, you will have very high membrane potential, event two ions difference can raise potential about 200 mV. In your case, I suppose 500 mV is not enough to separate all ions in a PBC box. https://www.mpibpc.mpg.de/grubmueller/compel Harutyun Sahakyan Senior Assistant at Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology, NAS, Armenia, Yerevan Tel: +374 93 323990 h_sahak...@mb.sci.am sahakya...@gmail.com February 13, 2020 2:07 AM, "Live King" wrote: > Dear all, > > I am running a simple test case with a lipid bilayer (DMPC), water, and > ions (150mM KCL) under the influence of a constant electric field ( 300mV, > 500mV, and 700mV). *I expected positive and negative ions to separate in > the presence of an external electric field*. However, I am not observing > such behavior despite running the all-atom simulation for 400ns in any > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui > production with electric field option. > > for example 500mV electric field in Z-direction : > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = > 500 mV * > > Are there any settings to run the electric field simulation that I miss? > Any help will be greatly appreciated. > > Thank you, > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to > gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can't observe ion separation under the influence of electric field
Den 2020-02-12 kl. 23:07, skrev Live King: Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not observing such behavior despite running the all-atom simulation for 400ns in any case. I am using gromacs 2018.2, my mdp file is standard charmm-gui production with electric field option. for example 500mV electric field in Z-direction : electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = 500 mV * Are there any settings to run the electric field simulation that I miss? Any help will be greatly appreciated. Did you make density plots to check? Do you get an output field.xvg that prints the field strength? It may be optional though. The force on the atoms will be quite small still compared to interatomic forces therefore the effect may be limited. F = q E (convert to right units). In GROMACS MD units a typical interatomic force is ~ 1000 kJ/mol/nm^2. Thank you, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Can't observe ion separation under the influence of electric field
Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not observing such behavior despite running the all-atom simulation for 400ns in any case. I am using gromacs 2018.2, my mdp file is standard charmm-gui production with electric field option. for example 500mV electric field in Z-direction : electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = 500 mV * Are there any settings to run the electric field simulation that I miss? Any help will be greatly appreciated. Thank you, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
